BP_PAPPLMAKER(1) User Contributed Perl Documentation BP_PAPPLMAKER(1)NAME
papplmaker.PLS - Analysis tools module generator
SYNOPSIS
# get some help
papplmaker.PLS -h
# generate module for program 'seqret'
papplmaker.PLS -n edit.seqret
# ditto, but specify where to find 'seqret'
papplmaker.PLS -n edit::seqret
-l http://localhost:8080/axis/services
# ditto, but specify a non-default access method to 'seqret'
papplmaker.PLS -n edit::seqret
-l http://corba.ebi.ac.uk/IOR/Analyses.ref
-a corba
# generate modules for all available analyses
# (using default location and default access method)
papplmaker.PLS
# do not generate but see what would be generated
papplmaker.PLS -s
papplmaker.PLS -S
# generate module for analysis 'edit::seqret'
# but name it 'MySeqret'
papplmaker.PLS -n edit::seqret -m MySeqret
# ...and use it
use MySeqret;
print new MySeqret->sequence_direct_data ('tatatacccgt')
->osformat ('embl')
->wait_for
->outseq;
# ditto but put the result into directory '/tmp/my'
# (directories do not need to exist)
papplmaker.PLS -n edit::seqret -m MySeqret -d /tmp/my/
# generate modules for all analysis whose names
# matches given regular expression (case insensitive)
papplmaker.PLS -r 'edit'
# ditto, but name generated module with your own names
# (letting papplmaker.PLS substitute parts of your names)
papplmaker.PLS -r 'edit' -m 'My_$ANALYSIS'
DESCRIPTION
The module "Bio::Tools::Run::Analysis" provides access to the local and
remote analysis tools in a unified way (defined in "Bio::AnalysisI").
The module uses general approach allowing to set arbitrary input data
and to retrieve results by naming them. However, sometimes is more
convenient to use a specific module, representing one analysis tool,
that already knows about available input and result names.
The generator "papplmaker.PLS" creates such dedicated modules.
"papplmaker.PLS" uses the same access method as the general module -
which means that depending on the parameter "access" it can use SOAP,
CORBA or any other (supported) protocol, or it can access local
analysis (available on the same machine where "papplmaker.PLS" is
invoked).
"papplmaker.PLS" does its job either for one named analysis (specified
by the "-n" option, or it uses "Bio::Tools::Run::AnalysisFactory"
module in order to find what analyses are available, and can limit
their number by matching against a regular expression given by the "-r"
option.
The generated module or modules are named by default similarly to the
names of the corresponding analyses, but this can be changed by the
"-m" option which is actually a template where the following strings
are recognised and replaced:
$ANALYSIS or ${ANALYSIS}
Will be replaced by the name of the analysis.
$CATEGORY or ${CATEGORY}
Will be replaced by the name of the category where the analysis
belongs to.
$SERVICE or ${SERVICE}
Will be replaced by the entire name of the service (which is
usually a concatenation of a category and a analysis name, and it
is used also as a default module name, btw).
What is a difference between the "service" and "analysis", and what
does "category" mean? Sometimes these terms may be confusing because
they may mean slightly different things depending on the access method
used to communicate with them. Generally, an "analysis" is a program
(an application, a tool) running somewhere, but sometimes on a local
machine. An example of an analysis is "seqret" (from the EMBOSS
package). The analyses can be grouped into categories by their
functions or by type of data they deal with (but sometimes there are no
categories at all). Each analyses can be accessed using a higher level
of abstraction, a "service". A service is usually a protocol-dependent
wrapper, such as a Web Service, or a CORBA service. For example there
is a "edit::seqret" service which represents analysis "seqret" in the
category "edit".
FEEDBACK
Mailing Lists
User feedback is an integral part of the evolution of this and other
Bioperl modules. Send your comments and suggestions preferably to the
Bioperl mailing list. Your participation is much appreciated.
bioperl-l@bioperl.org - General discussion
http://bioperl.org/wiki/Mailing_lists - About the mailing lists
Reporting Bugs
Report bugs to the Bioperl bug tracking system to help us keep track of
the bugs and their resolution. Bug reports can be submitted via the
web:
http://bugzilla.open-bio.org/
AUTHOR
Martin Senger (senger@ebi.ac.uk)
COPYRIGHT
Copyright (c) 2003, Martin Senger and EMBL-EBI. All Rights Reserved.
This script is free software; you can redistribute it and/or modify it
under the same terms as Perl itself.
DISCLAIMER
This software is provided "as is" without warranty of any kind.
BUGS AND LIMITATIONS
None known at the time of writing this.
perl v5.14.1 2011-07-21 BP_PAPPLMAKER(1)
